Article
Chemistry, Multidisciplinary
Baptiste Moge, Baptiste Schindler, Oznur Yeni, Isabelle Compagnon
Summary: Using ion vibrational spectroscopy, researchers determine the structure and linkage of fucosylated fragments of glycans and discover a new type of fucose migration. This research provides insights into the characterization of glycans and the underlying processes in mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Jiyeon Lee, Dahye Im, Yajie Liu, Jing Fang, Xibao Tian, Minsu Kim, Wen-Bin Zhang, Jongcheol Seo
Summary: A technique combining ion mobility spectrometry-mass spectrometry (IMS-MS) and supercharging electrospray ionization (ESI) has been demonstrated to effectively differentiate protein chemical topology. By incorporating as many charges as possible into proteins via supercharging ESI, the protein chains can be largely unfolded and stretched, revealing their hidden chemical topology. Different chemical topologies result in different geometric sizes of the unfolded proteins due to constraints in torsional rotations. The introduction of new topological indices allows for successful differentiation of various protein chemical topologies. This technique provides an easy classification of the topological features of complex proteins, previously concealed by their inherent complexity, and establishes a visual standard for discerning protein topologies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Kim Greis, Carla Kirschbaum, Giulio Fittolani, Eike Mucha, Rayoon Chang, Gert von Helden, Gerard Meijer, Martina Delbianco, Peter H. Seeberger, Kevin Pagel
Summary: This study investigates the influence of fluorination on the structure of the glycosyl cation, an intermediate in glycosylation reactions. The results reveal that C3 and C6 fluorination of glucosyl building blocks can alter the structure of the glycosyl cation, with neighboring group participation being the dominant motif.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yu-Chieh Huang, Pierre Tremouilhac, An Nguyen, Nicole Jung, Stefan Braese
Summary: ChemSpectra is a web-based software that visualizes and analyzes spectroscopic data, integrating solutions for various types of spectroscopy. It supports open file formats and can be extended to read other formats, making data interoperable and accessible for further analysis and research.
JOURNAL OF CHEMINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Maike Lettow, Kim Greis, Eike Mucha, Tyler R. Lambeth, Murat Yaman, Vasilis Kontodimas, Christian Manz, Waldemar Hoffmann, Gerard Meijer, Ryan R. Julian, Gert von Helden, Mateusz Marianski, Kevin Pagel
Summary: Fucose is a signaling carbohydrate attached to the end of glycan processing. It has various roles in processes like leukocyte adhesion and pathogen-receptor interactions. However, the presence of fucose-containing chimeric fragments in mass-spectrometric analysis has complicated the determination of glycans' structure. In this study, various techniques were used to deduce the rearrangement product of fucose in model trisaccharides Lewis x and blood group H2, with the most likely product being fucose attached to galactose through an alpha(1 -> 6) glycosidic bond.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: Daptomycin is a cyclic lipopeptide antibiotic that interacts with lipid membranes in a non-specific manner. The interaction strength depends on membrane rigidity, with more rigid membranes showing stronger interactions. More fluid membranes may undergo pore formation to expose daptomycin to oxidation. These findings highlight the complementary use of native mass spectrometry, fast photochemical oxidation of peptides, and membrane conductance experiments in studying antibiotic-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Shichen Su, Shanshan Li, Ting Deng, Minsong Gao, Yue Yin, Baixing Wu, Chao Peng, Jianzhao Liu, Jinbiao Ma, Kaiming Zhang
Summary: This study reveals the structure and function of the m(6)A writer complex. Cryo-EM and other experimental methods were used to uncover the structure of MACOM and its interaction with MAC.
Article
Chemistry, Multidisciplinary
Daniele Ubbiali, Marta Fratini, Lolita Piersimoni, Christian H. Ihling, Marc Kipping, Ingo Heilmann, Claudio Iacobucci, Andrea Sinz
Summary: The conformational ensemble of alpha-synuclein shifts during liquid-liquid phase separation, and a novel mass spectrometry-based approach is established to solve open questions in LLPS structural biology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Mathias Paul, Katrin Peckelsen, Thomas Thomulka, Jonathan Martens, Giel Berden, Jos Oomens, Joerg-M. Neudoerfl, Martin Breugst, Anthony J. H. M. Meijer, Mathias Schaefer, Albrecht Berkessel
Summary: The study reported in this paper focuses on the preparation of charge-tagged Breslow intermediates/keto tautomers derived from three different types of NHCs and aldehydes. Using ESI-MS IR ion spectroscopy, it was confirmed that in the gas phase, the Breslow intermediates derived from imidazolidin-2-ylidenes exist as diamino enols, while those derived from 1,2,4-triazolin-5-ylidenes and thiazolin-2-ylidenes exist as keto tautomers. This observation is consistent with findings in solution and in the crystalline state.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Takashi Matsui, Eiji Kojitani, Taichi Takasawa, Arisa Suto, Ami Tamari, Go Watanabe, Yoshio Kodera
Summary: Structural proteomics techniques are valuable in identifying protein binding sites. This study analyzed the solvent-accessible surface of human serum albumin using covalent protein labeling and compared it to surfaces derived from 27 PDB structures. The results revealed inconsistencies in solvent-accessible surface area values calculated from PDB structures, which are attributed to the lack of PDB data representing structures in solution.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Martijn M. Vanduijn, Hendrik-Jan Brouwer, Pablo Sanz de la Torre, Jean-Pierre Chervet, Theo M. Luider
Summary: The research team reported an improved electrochemical method that achieves complete reduction of both intermolecular and intramolecular disulfide bridges in a set of monoclonal antibodies. The method utilizes an online electrochemical flow cell to provide information on the pairing of heavy and light chains in the antibodies. The complete reduction of intramolecular disulfide bridges is important for the intact mass of the antibody chain and the confirmation of the protein's amino acid sequence.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Lu Li, Cuiji Sun, Yaoting Sun, Zhen Dong, Runxin Wu, Xiaoting Sun, Hanbin Zhang, Wenhao Jiang, Yan Zhou, Xufeng Cen, Shang Cai, Hongguang Xia, Yi Zhu, Tiannan Guo, Kiryl D. Piatkevich
Summary: This paper describes a spatially resolved proteomics method called Expansion Proteomics (ProteomEx), which combines tissue expansion with mass spectrometry-based proteomics. The method allows quantitative profiling of proteome variability in mammalian tissues using manual microsampling, without the need for custom equipment. The authors validated the method by analyzing brain, liver, and breast cancer samples, and demonstrated its utility by identifying proteins associated with Alzheimer's disease in a mouse model.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Roderick Corstiaan Abraham Versloot, Patricia Arias-Orozco, Matthijs Jonathan Tadema, Florian Leonardus Rudolfus Lucas, Xinghong Zhao, Siewert J. J. Marrink, Oscar Paul Kuipers, Giovanni Maglia
Summary: Mass spectrometry cannot distinguish between molecules with the same mass-to-charge ratio, but nanopore technology can differentiate diastereomeric and enantiomeric differences in peptides that cannot be observed by conventional MS analysis. The resolution in nanopore analysis is likely due to multiple chiral interactions during peptide transport across the nanopore, similar to chiral chromatography. Nanopore technology also offers possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Corinne A. Lutomski, Tarick J. El-Baba, Joshua D. Hinkle, Idlir Liko, Jack L. Bennett, Neha V. Kalmankar, Andrew Dolan, Carla Kirschbaum, Kim Greis, Leonhard H. Urner, Parth Kapoor, Hsin-Yung Yen, Kevin Pagel, Christopher Mullen, John E. P. Syka, Carol V. Robinson
Summary: By using an infrared laser in a high-pressure linear ion trap, researchers were able to remove detergent micelles and obtain good sequence coverage for membrane proteins and their complexes through top-down mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Clinical Neurology
Jijing Wang, Cong Guo, Zhaowei Meng, Marissa D. Zwan, Xin Chen, Sven Seelow, Susanna L. Lundstrom, Sergey Rodin, Charlotte E. Teunissen, Roman A. Zubarev
Summary: This study strengthens the association between isoAsp and Alzheimer's disease (AD) using novel approaches to isoAsp analysis in blood samples. The findings demonstrate elevated isoAsp levels, reduced anti-isoAsp antibodies, increased A beta concentration, and more protein aggregation in AD blood compared to controls. Additionally, deamidation reduces the binding capacity of blood protein HSA with A beta and p-tau.
ALZHEIMERS & DEMENTIA
(2023)
Article
Chemistry, Analytical
Akos Vegvari, Jimmy E. Rodriguez, Roman A. Zubarev
Summary: Chemical proteomics investigates the impact of drugs on cellular proteomes. Single-cell proteomics analysis is necessary due to the complexity and diversity of tumors. Single-cell chemical proteomics (SCCP) has become quantitative enough to study the effects of drugs on target proteins, revealing the heterogeneous response of cancer cells.
ANALYTICAL CHEMISTRY
(2022)
Article
Energy & Fuels
J-F. Fortune, P. Cologon, P. Hayrault, M. Heninger, J. Leprovost, J. Lemaire, P. Anselmi, M. Matrat
Summary: This study evaluates the impact of ethanol content on emissions of recent vehicle technologies. The results show negligible impact on emissions for ethanol content from 10 to 20% vol. However, significant emission composition variation is observed at higher ethanol concentrations.
Article
Biochemical Research Methods
Zeljka Popovic, Lissa C. Anderson, Xuepei Zhang, David S. Butcher, Greg T. Blakney, Roman A. Zubarev, Alan G. Marshall
Summary: Isotopic depletion of growth medium improves protein mass measurement accuracy and signal-to-noise ratio, enabling better mass spectrometry analysis for both bacteria and eukaryotes.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Immunology
Abdul Muktadir Shafi, Akos Vegvari, Roman A. Zubarev, Carlos Penha-Goncalves
Summary: This study reveals the important role of the STING-INFb-CXCL10 pathway in brain microvascular endothelial cells (BECs) in the development of cerebral malaria (CM). Activation of this pathway leads to immunoproteasome activation, enhanced antigen presentation, and impairment of endothelial barrier function. These findings provide insights into the pathogenesis of CM and its lethality.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Medicine, Research & Experimental
Huqiao Luo, Vilma Urbonaviciute, Amir Ata Saei, Hezheng Lyu, Massimiliano Gaetani, Akos Vegvari, Yanpeng Li, Roman A. Zubarev, Rikard Holmdahl
Summary: Mutations in NCF1 gene that cause low production of ROS are strongly linked to systemic lupus erythematosus. The deficiency of ROS in plasmacytoid dendritic cells (pDCs) exacerbates lupus development by promoting pDC accumulation in multiple organs, elevating IFN-alpha levels, and activating IFN-stimulated genes. Mechanistic studies show that ROS deficiency enhances pDC generation and migration, which further augment type I IFN responses. Restoring NOX2-derived ROS specifically in pDCs protects against lupus by suppressing these pathways.
Article
Hematology
Anna Rydstrom, Tan H. M. Grahn, Abhishek Niroula, Els Mansell, Mark van der Garde, Maroulio Pertesi, Agatheeswaran Subramaniam, Shamit Soneji, Roman Zubarev, Tariq Enver, Bjorn Nilsson, Kenichi Miharada, Jonas Larsson, Stefan Karlssona
Summary: This study provides a detailed functional and molecular characterization of HSCs at different phases of regeneration and identifies a gene set associated with the transition from proliferation to quiescence.
EXPERIMENTAL HEMATOLOGY
(2023)
Article
Immunology
Mike Aoun, Ana Coelho, Alexander Kramer, Amit Saxena, Pierre Sabatier, Christian Michel Beusch, Erik Lonnblom, Manman Geng, Nhu-Nguyen Do, Zhongwei Xu, Jingdian Zhang, Yibo He, Laura Romero Castillo, Hassan Abolhassani, Bingze Xu, Johan Viljanen, Joanna Rorbach, Gonzalo Fernandez Lahore, Inger Gjertsson, Alf Kastbom, Christopher Sjowall, Jan Kihlberg, Roman A. Zubarev, Harald Burkhardt, Rikard Holmdahl
Summary: The study reveals that autoreactive antigen-specific naive B cells tolerize infiltrating T cells against self-antigens to impede the development of tissue-specific autoimmune inflammation.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biochemical Research Methods
Akos Vegvari, Xuepei Zhang, Roman A. Zubarev
Summary: This study successfully detected proteins from individual Escherichia coli bacteria for the first time, with validation of the findings through comparison with other samples and bulk proteomics data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemical Research Methods
Irina D. D. Vasileva, Tatiana Yu. Samgina, Zhaowei Meng, Roman A. A. Zubarev, Albert T. T. Lebedev
Summary: In traditional proteomic analysis, disulfide bonds in peptides pose a problem for sequencing, requiring multiple reaction steps. However, this study found that EThcD technology can sequence peptides with disulfide bonds without the need for chemical derivatization.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Tatiana Yu. Samgina, Irina D. Vasileva, Polonca Trebse, Gregor Torkar, Alexey K. Surin, Zhaowei Meng, Roman A. Zubarev, Albert T. Lebedev
Summary: Peptides released on frogs' skin in a stress situation are their only weapon against micro-organisms and predators. Each frog population has its own unique peptidome suitable for their habitat. This study analyzed the peptidome composition of the Central Slovenian agile frog population, and discovered multiple peptide families.
Article
Biochemistry & Molecular Biology
Amir Ata Saei, Hassan Gharibi, Hezheng Lyu, Brady Nilsson, Maryam Jafari, Hans Von Holst, Roman A. Zubarev
Summary: The study investigated the molecular consequences of traumatic brain injuries using a proteomics approach. It found that dynamic impacts led to reduced neuron viability and significant changes in protein solubility. The affected proteins were involved in various pathways, including cell adhesion, stress response, immune response, complement, and coagulation cascades.
Article
Multidisciplinary Sciences
Shane C. Wright, Aikaterini Motso, Stefania Koutsilieri, Christian M. Beusch, Pierre Sabatier, Alessandro Berghella, Elodie Blondel-Tepaz, Kimberley Mangenot, Ioannis Pittarokoilis, Despoina-Christina Sismanoglou, Christian Le Gouill, Jesper V. Olsen, Roman A. Zubarev, Nevin A. Lambert, Alexander S. Hauser, Michel Bouvier, Volker M. Lauschke
Summary: This study investigates the subcellular location of GLP-1R signaling events and reveals associations between signaling profiles and adverse drug reactions, providing important insights for rational drug design and improving the therapeutic potential of GLP-1R agonists.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Zhongwei Xu, Bingze Xu, Susanna L. Lundstrom, Alex Moreno-Giro, Danxia Zhao, Myriam Martin, Erik Lonnblom, Qixing Li, Alexander Kramer, Changrong Ge, Lei Cheng, Bibo Liang, Dongmei Tong, Roma Stawikowska, Anna M. Blom, Gregg B. Fields, Roman A. Zubarev, Rikard Holmdahl
Summary: This study developed antibodies targeting type-II collagen and investigated their mechanism of action. The antibody R69-4 inhibits autoantibody-mediated arthritis by hindering FCGR3 signaling, highlighting its potential clinical utility in acute rheumatoid arthritis.
NATURE COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Joel Lemaire, Michel Heninger, Essyllt Louarn, Ira Katz, Renaud Tissier, Matthieu Chalopin, Geraldine Farjot, Aude Milet
Summary: This paper presents a technique based on mass spectrometry for measuring argon solubility in liquids, including blood, which can be used in pharmacokinetics testing of argon. Results from sensitivity experiments using ambient air, water, and rabbit blood are reported based on a prototype, showing that the system was sensitive to argon during all of the testing. The authors believe that the technique and prototype of the quadrupole mass spectrometer gas analyzer will be capable of inferring argon pharmacokinetics through the analysis of blood samples.
MEDICAL GAS RESEARCH
(2023)
